1YYU

D100E Trichodiene Synthase: Complex With Mg, Pyrophosphate, and (4S)-7-azabisabolene

PDB DOI: 10.2210/pdb1YYU/pdb

Classification: LYASE
Organism(s): Fusarium sporotrichioides
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2005-02-25 Released: 2005-03-29
Deposition Author(s): Vedula, L.S., Rynkiewicz, M.J., Pyun, H.J., Coates, R.M., Cane, D.E., Christianson, D.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.255
R-Value Work: 0.218

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Molecular Recognition of the Substrate Diphosphate Group Governs Product Diversity in Trichodiene Synthase Mutants.

Vedula, L.S., Rynkiewicz, M.J., Pyun, H.J., Coates, R.M., Cane, D.E., Christianson, D.W.

(2005) Biochemistry 44: 6153-6163

PubMed: 15835903 Search on PubMed
DOI: 10.1021/bi050059o
Primary Citation of Related Structures:
1YJ4, 1YYQ, 1YYR, 1YYS, 1YYT, 1YYU

PubMed Abstract:

The X-ray crystal structures of Y305F trichodiene synthase and its complex with coproduct inorganic pyrophosphate (PP(i)) and of Y305F and D100E trichodiene synthases in ternary complexes with PP(i) and aza analogues of the bisabolyl carbocation intermediate are reported. The Y305F substitution in the basic D(302)RRYR motif does not cause large changes in the overall structure in comparison with the wild-type enzyme in either the uncomplexed enzyme or its complex with PP(i). However, the loss of the Y305F-PP(i) hydrogen bond appears to be compensated by a very slight shift in the position of the side chain of R304. The putative bisabolyl carbocation mimic, R-azabisabolene, binds in a conformation and orientation that does not appear to mimic that of the actual carbocation intermediate, suggesting that the avid inhibition by R- and S-azabisabolenes arises more from favorable electrostatic interactions with PP(i) rather than any special resemblance to a reaction intermediate. Greater enclosed active-site volumes result from the Y305F and D100E mutations that appear to confer greater variability in ligand-binding conformations and orientations, which results in the formation of aberrant cyclization products. Because the binding conformations and orientations of R-azabisabolene to Y305F and D100E trichodiene synthases do not correspond to binding conformations required for product formation and because the binding conformations and orientations of diverse substrate and carbocation analogues to other cyclases such as 5-epi-aristolochene synthase and bornyl diphosphate synthase generally do not correspond to catalytically productive complexes, we conclude that the formation of transient carbocation intermediates in terpene cyclization reactions is generally under kinetic rather than thermodynamic control.

Organizational Affiliation:

Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trichodiene synthase	A, B	374	Fusarium sporotrichioides	Mutation(s): 1 Gene Names: TRI5, TOX 5 EC: 4.2.3.6
UniProt
Find proteins for P13513 (Fusarium sporotrichioides) Explore P13513 Go to UniProtKB: P13513
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13513
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAZ Query on SAZ Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B]	J [auth B]	(1S)-N,4-DIMETHYL-N-(4-METHYLPENT-3-ENYL)CYCLOHEX-3-ENAMINIUM C₁₄ H₂₆ N GGPFTSMJRHEOJG-AWEZNQCLSA-O		Ligand Interaction
RAZ Query on RAZ Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	(1R)-N,4-DIMETHYL-N-(4-METHYLPENT-3-ENYL)CYCLOHEX-3-ENAMINIUM C₁₄ H₂₆ N GGPFTSMJRHEOJG-CQSZACIVSA-O		Ligand Interaction
POP Query on POP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B]	F [auth A], K [auth B]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B]	G [auth A], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B]	C [auth A], D [auth A], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction